Molecular Genetics MCB6937 Syllabus 2018

-Updated Jan 6, 2018

Molecular Genetics MCB6937 Syllabus 2018

version 2

Course/Section Information: MCB69372 Spring 2018-sections 1171 and 1D96

Course Prerequisites: BSC 2010 and BSC 2010L, or equivalent, with minimum grades of C.

Instructors: Dr. William Gurley (Department of Microbiology & Cell Science)

Textbook: Lewin's Genes or XI or XII, (strongly recommended, but not required), Authors: Kreb, Goldstein and Kilpatrick

Introduction: This course will discuss the synthesis and manipulation of DNA and the principles of gene expression at the molecular level in both prokaryotes and eukaryotes. The topics covered will include an introduction to the concepts of DNA replication, repair and packaging of the genome into chromosomes. In preparation for this course, you should have an understanding of basic college level introductory biology and it is recommended to have at least one other more specialized biology course such as Microbiology, Botany, Zoology, Genetics or Biochemistry.

Student Learning Goals:

The goal of PCB4522 (Molecular Genetics) is for participants to understand the roles of DNA and RNA in both prokaryotes (eubacteria and Archaea) and eukaryotes, including yeast, plants, drosophila and man. Students will:

1. Develop an appreciation of the organization and evolution of living systems and the role of genetic mutation and selection in the evolution of the human species.

2. Acquire knowledge regarding DNA replication in bacteria, plasmids, transposable elements, as well as eukaryotic organelles and the nucleus.

3. Become familiar with the molecular events involved in DNA repair and recombination. 4. Acquire a detailed understanding of the molecular mechanisms related to gene

expression at the transcriptional level, with an emphasis on eukaryotes. 5. Learn to extract information from genomic databases and perform DNA sequence

analyses using online bioinformatics tools.

Presentation Format: This course will be a hybrid between an online course and a traditional lecture style course. The goal is to have all lecture material recorded live each lecture and posted here at the Canvas website or at . There will be approximately 3 hours of recorded lecture material available each week.

Attendance: optional though encouraged; web and distance students may also attend as seating permits. The class meets on Tuesdays period 7 (1:55-2:45 pm) and Thursdays periods 7-8 (1:553:50 pm). A 5 min stretch break will be given on Thursdays at 3 pm.

Office hours: Fridays 4-6+ pm Email the instructor for an appointment time. Campus and local students are welcome to drop by my office (room 1152, MCS Building) for meetings on Friday afternoons. Distance students can meet using the Canvas Conference feature.

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Honor Code violations: Exams 1, 2, 3, 4, and the Optional Final are closed book and no outside material may be used during the exam including web-based and printed materials. Communication with persons not involved in proctoring is also prohibited during the exam. Failure to comply will result in a failing grade for the course.

Computer requirement: All exams will be administered through ProctorU using Canvas in E-learning with students using personal computers. The exam may be taken at any location approved by ProctorU during the regularly scheduled course times. All students (campus and distance) will be given at least a 48 hr window to take the exams.

The major exams can only be taken at the listed times (below) unless special arrangements are made prior to the exam with the instructor.

All exams will be proctored with using ProctorU. The use of multiple devices to take exams and attempts to Screen Print during exams is strictly forbidden and will be prosecuted as Honor Code violations. Anyone not able to meet the above laptop computer requirements should contact the instructor as soon as possible.

ProctorU requirements: In an effort to enhance the integrity of the assessment process, USB external cameras will be required for all distance-proctored exams. A goose-neck model works best and may be acquired for around $50. Students not seeking financial hardship assistance should contact the instructor before the first exam.

Spring 2018 Exam Calendar:

Exam 1 Jan 20-22 (6 hr of material) Exam 2 Feb 17-19 (10 hr of material) Exam 3 Mar 17-19 (11 hr of material) Exam 4 Apr 14-16 (12 hr of material) (Total from Exams + 90%)

(13.84% of grade) ProctorU (23.08% of grade) ProctorU (25.39% of grade) ProctorU (27.69% of grade) ProctorU

Homework quizzes (2% of grade) online submission; multiple attempts allowed

Gene structure/bioinformatics (3% of grade) online submission

Genome engineering project (5% of grade) online submission

Note: You may substitute the Final (retake exam) for the regular exam having the lowest score. However, if the score on the Final (re-take exam) is lower than your original grade, the original grade will stand.

Grading Policies:

4 Major Exams: 95 points. There will be four major exams plus an optional Final exam. The Final is actually just a retake of your lowest exam. The questions will be drawn from 15-18 questions banks per exam (40 multiple choice and fill-in-the-blank), so no two exams or re-takes are the same. Note: the exams are not of equal weight. Exam 1 is worth only ~50% of Exam 4. The exam weights are proportional to the number of lecture hours of material covered.

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Homework assessments: 2.0 points. A perfect score will equal 2.0 points on all homework assessments. Homework assessments are open book exercises to encourage you to read the lecture material before or during the week the topic is covered in lecture. The best way to use the Homework quizzes is to take them multiple times to uncover all the questions. Use them to study using no notes to identify gaps in your knowledge.

Gene Structure/Bioinformatics Project: 3 points. This will begin after Exam 1. You will be assigned an unknown cDNA and expected to identify the gene and organism. In addition, you will learn how to conduct a multiple sequence alignment using web-based tools

The optional Genome Engineering Project will have multiple parts with the total points to equal 5.00 towards the final course grade as extra credit.

There will be no grade curve. (36% of the class has earned an "A" for the last 3 years.)

Grading Scale Numerical Equivalents

A = 91 or above

C = 68-73.99(minimum needed for major)

A- = 89-90.99

C- = 65-67.99

B+ = 85-88.99

D+ = 62-64.99

B = 81-84.99

D = 58-61.99

B- = 79-80.99

D- = 54-57.99

C+ = 74-78.99

E = 0-53.99

UF Grading Policies:



Schedule of lecture topics:

(Note: This schedule is only approximate and will vary according to the amount of material covered in class between Exams.)

Quick Guide to lecture topics:

Module 1: Evolution of early man: culture as phenotype? Replication of the genome (bacteria & eukaryotes) Extrachromosomal replicons (plasmids, mitochondria) Agrobacterium tumor-inducing plasmid Bacterial cell cycle and ColE1 replication mechanism

Module2: DNA replication details of mechanism and proteins involved Recombination in bacteria and eukaryotes DNA-based Transposons in bacteria Eukaryotic Transposons (DNA-based) Retrotransposons and Retroviruses (eukaryotes)

Module 3: DNA repair systems (bacterial and eukaryotic) Bacterial Transcription

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promoters, RNA polymerase structure, sigma structure, termination, rho The Operon (basic concepts, CAP regulation, Lac, Ara and Trp) Module 4: Chromosomes Histones and nucleosomes Eukaryotic Transcription Gene structure and promoters Basal factors: TFIID, TFIIH, TFIIB, Mediator, preinitiation complex Eukaryotic transcriptional regulation DNA binding domains, steroid receptors, activators & repressors Plant transcription Epigenetics RNA-based silencing, X-chromosome inactivation, transcriptional memory, silencing of ancient transposons

Exam 1 Text Material

Genes XI Chapter 11 (The Replicon) Chapter 12 (Extrachromosomal replicons) Parts of Chapter 13 (Bacterial replication connected to cell cycle) as follows: Introduction

______Genes XI ________________

Exam 2 Text Material

Genes X (current text) Chapter 14 (DNA Replication) Sections 14.1-14.16 (skip 14.15) Chapter 15 (Homologous and site-specific recombination) Sections 15.1-15.14 Chapter 17 (Transposable elements and retroviruses) Sections 17.1-17.20, skip 17.17 (revised 14Feb2011)

Exam 3 Text Material (subject to revision; check Announcements)

Genes X (current text) Chapter 16 Repair Systems (all sections) Chapter 19 Prokaryotic Transcription Chapter 26 The Operon (all sections except 26.15)

______Earlier editions: _________________ Genes IX Chapter 20 Repair (all sections) Chapter 11 Transcription (all sections) chapter 12 The Operon (sections 12.1 through 12.21)

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Chapter 28 Chromosomes (all sections except skip 28.8)

2018 Spring Break (March 3rd through March 10th)

Exam 4 Text Material (subject to revision; check Announcements)

Genes X (current text) Chapter 9 Chromosomes (all sections except 9.8) Chapter 10 Chromatin (sections 10.1-10.8; 10.10) Chapter 20 Eukaryotic Transcription (all sections) Transcription Factors (PowerPoint slides)

______Earlier editions: _________________ Genes IX chapter 29 Nucleosomes sections: 29.1 through 29.4 29.7 through 29.9 29.11 through 29.13

Genes VIII chapter 20 Nucleosomes sections: 20.1 through 20.4 20.7 through 20.10 (skip 20.9) 20.12 through 20.13

Genes IX chapter 24 Promoters and Enhancers Sections: 24.1 through 24.20 (all sections)

Notes: 1) For the last lecture section (Activating Transcription), the exam questions will all come from the lecture notes. The textbook is still relevant, but only as a resource if there are topics in the slides that are unclear.

2) The topic selection for lecture is subject to change at the instructor discretion. Students will be given advance notice of changes to accommodate their study and exam preparation.

Policy regarding letters of recommendation 2018

The Department of Microbiology & Cell Science policy on letters of recommendation advises instructors not to provide letters in classes of 50 or more students due to the impossibility of providing meaningful evaluations.

Unfortunately, due to the large number of students enrolled in this course (180), I will not be able to provide letters of recommendation. This is a reversal of my past policy where letters were usually provided upon request. The demand for spring 2009 (PCB4522) was for 78 letters. Each letter was allotted a 30 min interview where I tried to assess qualities such as leadership,

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